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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 1-153818821-ACT-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=153818821&ref=ACT&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 153818821,
"ref": "ACT",
"alt": "A",
"effect": "frameshift_variant",
"transcript": "ENST00000368655.5",
"consequences": [
{
"aa_ref": "S",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATAD2B",
"gene_hgnc_id": 30778,
"hgvs_c": "c.565_566delAG",
"hgvs_p": "p.Gln190fs",
"transcript": "NM_020699.4",
"protein_id": "NP_065750.1",
"transcript_support_level": null,
"aa_start": 189,
"aa_end": null,
"aa_length": 593,
"cds_start": 565,
"cds_end": null,
"cds_length": 1782,
"cdna_start": 807,
"cdna_end": null,
"cdna_length": 7475,
"mane_select": "ENST00000368655.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATAD2B",
"gene_hgnc_id": 30778,
"hgvs_c": "c.565_566delAG",
"hgvs_p": "p.Gln190fs",
"transcript": "ENST00000368655.5",
"protein_id": "ENSP00000357644.4",
"transcript_support_level": 1,
"aa_start": 189,
"aa_end": null,
"aa_length": 593,
"cds_start": 565,
"cds_end": null,
"cds_length": 1782,
"cdna_start": 807,
"cdna_end": null,
"cdna_length": 7475,
"mane_select": "NM_020699.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATAD2B",
"gene_hgnc_id": 30778,
"hgvs_c": "c.565_566delAG",
"hgvs_p": "p.Gln190fs",
"transcript": "ENST00000634544.1",
"protein_id": "ENSP00000489184.1",
"transcript_support_level": 5,
"aa_start": 189,
"aa_end": null,
"aa_length": 593,
"cds_start": 565,
"cds_end": null,
"cds_length": 1782,
"cdna_start": 759,
"cdna_end": null,
"cdna_length": 2342,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATAD2B",
"gene_hgnc_id": 30778,
"hgvs_c": "c.565_566delAG",
"hgvs_p": "p.Gln190fs",
"transcript": "ENST00000634408.1",
"protein_id": "ENSP00000489595.1",
"transcript_support_level": 5,
"aa_start": 189,
"aa_end": null,
"aa_length": 577,
"cds_start": 565,
"cds_end": null,
"cds_length": 1734,
"cdna_start": 577,
"cdna_end": null,
"cdna_length": 1825,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATAD2B",
"gene_hgnc_id": 30778,
"hgvs_c": "c.142_143delAG",
"hgvs_p": "p.Gln49fs",
"transcript": "ENST00000703630.1",
"protein_id": "ENSP00000515408.1",
"transcript_support_level": null,
"aa_start": 48,
"aa_end": null,
"aa_length": 263,
"cds_start": 142,
"cds_end": null,
"cds_length": 793,
"cdna_start": 471,
"cdna_end": null,
"cdna_length": 1121,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATAD2B",
"gene_hgnc_id": 30778,
"hgvs_c": "c.568_569delAG",
"hgvs_p": "p.Gln191fs",
"transcript": "XM_047426115.1",
"protein_id": "XP_047282071.1",
"transcript_support_level": null,
"aa_start": 190,
"aa_end": null,
"aa_length": 594,
"cds_start": 568,
"cds_end": null,
"cds_length": 1785,
"cdna_start": 940,
"cdna_end": null,
"cdna_length": 7608,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATAD2B",
"gene_hgnc_id": 30778,
"hgvs_c": "c.565_566delAG",
"hgvs_p": "p.Gln190fs",
"transcript": "XM_047426117.1",
"protein_id": "XP_047282073.1",
"transcript_support_level": null,
"aa_start": 189,
"aa_end": null,
"aa_length": 593,
"cds_start": 565,
"cds_end": null,
"cds_length": 1782,
"cdna_start": 960,
"cdna_end": null,
"cdna_length": 7628,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000291199",
"gene_hgnc_id": null,
"hgvs_c": "n.297-9141_297-9140delCT",
"hgvs_p": null,
"transcript": "ENST00000820544.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 743,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATAD2B",
"gene_hgnc_id": 30778,
"hgvs_c": "c.*2_*3delAG",
"hgvs_p": null,
"transcript": "ENST00000634401.1",
"protein_id": "ENSP00000489313.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 186,
"cds_start": -4,
"cds_end": null,
"cds_length": 563,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 867,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GATAD2B",
"gene_hgnc_id": 30778,
"dbsnp": "rs886037647",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 6.152,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000368655.5",
"gene_symbol": "GATAD2B",
"hgnc_id": 30778,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.565_566delAG",
"hgvs_p": "p.Gln190fs"
},
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000820544.1",
"gene_symbol": "ENSG00000291199",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.297-9141_297-9140delCT",
"hgvs_p": null
}
],
"clinvar_disease": "Severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2",
"phenotype_combined": "Severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}